One common pain point for molecular modelers is discovering—too late—that a simulation fails because of issues in the structural model. Whether you’re preparing a protein-ligand complex or simulating a structure fetched from a public database, overlooked details like alternate locations, non-standard residues, or atomic clashes can derail hours of work.
SAMSON, the integrative molecular design platform, includes a set of structure preparation tools that can help avoid these frustrations. In particular, the Validate feature in the Home menu provides a fast, interactive way to inspect and correct common structural issues—before simulation or analysis begins.
What Does Validation Do?
The Validate tool, accessible via Home > Structures > Validate, checks your structure and helps fix:
- Alternate atomic locations (often from X-ray crystallography results)
- Non-standard residues not recognized by force fields
- Unusual bond lengths
- Clashes between atoms that may affect energy minimization or dynamics
These issues are particularly important when working with PDB or AlphaFold structures, which may include ambiguity or unresolved regions.
Why It Matters
Running simulations without validating your model can lead to errors or poor-quality results. For example, alternate locations may confuse energy minimizers that don’t know which atom to consider. Non-standard residues might lead to missing parameters in the force field. Structural clashes could result in extremely high energies or even crashes due to overlapping atoms.
Using Validate before starting your simulation helps ensure that what you’re simulating is coherent and realistic.
How to Use the Validation Tool
1. Open SAMSON and load your structure (either from your computer or use the Fetch command to retrieve it from the Protein Data Bank, AlphaFold DB, or another database).
2. Navigate to Home > Structures > Validate.
3. SAMSON will automatically check the model and highlight inconsistencies. You can then follow the suggested fixes to clean the model.
4. Combine this with other preparation tools—like Prepare to remove ligands or water, or Add hydrogens to ensure proper protonation.
Visual Overview
Tip: Combine with AlphaFold and Simulation
If you’re building models from sequences using AlphaFold or similar tools, consider validating the generated structure even if it comes from a high-quality model. This is especially useful before energy minimization or docking studies.
By integrating structure validation as a normal part of your workflow, you can save time, reduce errors, and start your simulations with higher-quality input models.
To explore the full range of interface tools, including structure preparation, AI tools, and simulation setup, visit the original documentation page:
https://documentation.samson-connect.net/users/latest/interface/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.